Carnitine (CAR), an amino acid derivative, has great potential as a facial exfoliating agent owing to its calcium chelating property under weakly acidic or neutral conditions. However, its application is limited by its poor transdermal penetration. To optimise its exfoliation efficacy with minimal concentration, we propose the ion-pair method. The ionic interaction between CAR and a zwitterionic substance was successfully monitored by measuring conductivity. The alterations of penetration and exfoliation efficacy for CAR addition to different types of counter ions were investigated in vitro and in vivo. We found that hydrogenated soya phosphatidylcholine (HSC), an amphiphilic counter ion, significantly increases the stratum corneum penetration and exfoliation efficacy of CAR. The changes of the CAR-HSC ionic interaction in the presence of calcium ions were also investigated by 1H nuclear magnetic resonance (NMR) spectroscopy. The NMR spectra for amino groups of CAR first decreased with HSC and then gradually recovered and shifted as calcium ions were added. From the results, a noble exfoliating complex of CAR with high exfoliation efficacy could be proposed. Moreover, the results demonstrate that NMR spectroscopy is useful to obtain direct experimental evidence of the molecular dynamics simulations of the alteration of an exfoliating complex as it penetrates.